There are two claims that define Process
Structuralism. First is that development has a strong influence on the kinds of
phenotypes available for selection, bringing developmental phenomena to bear on
evolutionary theory. Developmental processes are fundamentally developmental constraints
explaining biological phenomena, such as the conservation of traits across
phylogeny, in terms of developmental processes biasing the variation in phenotypic
forms available for selection. Distinctive is the second claim, the ontological
assertion that biological kinds can be individuated in terms of the kinds of
structures that emerge from the dynamic process of cellular and physiological development,
rather than in terms of historically contingent common descent. The dynamical
process of development generate stable archetypal organismic structures, these
constitute what was called a bauplan.

This book deals with embryology although it is not a book on embryology. It is in itself like a developing embryo and at a difference of textbooks it does not pretend to be an introduction to any particular scientific discipline. This work was born from a fascination about forms and it is the draft of a morphological process: the account of a form coming into being, the form of an as yet unnamed but emerging science. A new science of qualities (...) in which the natural phenomena are understood as wholes, as complex entities, possessing integral properties that are non-reducible to discrete or quantifiable magnitudes. This book is like a jump into the future of science but also it is a return in time in order to find the founder of science. The first thinker that blended speculative thought with the direct observation of facts. This book is a return to the organism, to purpose and meaning, a return to Aristotle. (shrink)

Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

The focus of this article is the analysis of generative mechanisms, a basic concept and phenomenon within the metatheoretical perspective of critical realism. It is emphasized that research questions and methods, as well as the knowledge it is possible to attain, depend on the basic view – ontologically and epistemologically – regarding the phenomenon under scrutiny. A generative mechanism is described as a trans empirical but real existing entity, explaining why observable events occur. Mechanisms are mostly possible to grasp only (...) indirectly by analytical work, based however on empirical observations. In order to achieve such an explanatory analysis, five methodological steps are suggested and discussed, among them abduction and retroduction. These steps are illustrated throughout by examples drawn from empirical research regarding social work practice. The article is concluded with a discussion of the need for knowledge of generative mechanisms. (shrink)

Developments in the sequencing of whole genomes and in simultaneously surveying many thousands of transcription and translation products of specific cells have ushered in a conceptual revolution in genetics that rationally introduces top-down, holistic analyses. This emphasized the futility of attempts to reduce genes to structurally discrete entities along the genome, and the need to return to Johannsen's definition of a gene as 'something' that refers to an invariant entity of inheritance and development. We may view genes either as generic (...) terms for units of inheritance whose referents are pragmatic ad hoc and context-dependent, or as (epistemologically) representing entities of cell functions. It is cellular functions that determine the structural referents along the DNA. Structures that happened to secure specific functions that were essential for or conducive to the survival of cells were selected for. With natural selection being the etiological background of genes as functions, genes obtain again their theoretical role as intervening variables, abstractive variables that purely 'summarize' characters. The importance of DNA sequences is that of all possible phenotypes these are the most basic ones from which we can read off the genotype directly. (shrink)

Chemical embryology was born in 1931 with the publication of Chemical Embryology by Joseph Needham. In the following two decades it became an innovative research project aiming at the description of the construction of the embryological structure and differentiation in biochemical terms. This research programme produced a vast amount of experimental evidence and theories on the chemical dynamics of the embryo: particularly chemical characterization of the zygote and the developing embryo, the chemical exchanges between the nucleus and the cytoplasm, the (...) significance of subcellular structures, and the role and distribution of nucleic acids within the cell. From the 1950s on, a large part of these results came to be integrated into the empirical basis of molecular biology. However, the shift from chemical embryology to molecular embryology was not just a semantic shift but a deep theoretical change, produced by the introduction of a new model of scientific explanation, based on the transmission and expression of genetic information and opposed to the biochemical definition of life. (shrink)

One of the most profound insights of the dynamic systems perspective is that new structures resulting from the developmental process do not need to be planned in advance, nor is it necessary to have these structures represented in genetic or neurological templates prior to their emergence. Rather, new structures can emerge as components of the individual and the environment self-organize; that is, as they mutually constrain each other's actions, new patterns and structures may arise. This theoretical possibility brings into developmental (...) theory the important concept of indeterminism--the possibility that developmental outcomes may not be predictable in any simple linear causal way from their antecedents. This is the first book to take a critical and serious look at the role of indeterminism in psychological and behavioral development. * What is the source of this indeterminism? * What is its role in developmental change? * Is it merely the result of incomplete observational data or error in measurement? It reviews the concepts of indeterminism and determinism in their historical, philosophical, and theoretical perspectives--particularly in relation to dynamic systems thinking--and applies these general ideas to systems of nonverbal communication. Stressing the indeterminacy inherent to symbols and meaning making in social systems, several chapters address the issue of indeterminism from metaphorical, modeling, and narrative perspectives. Others discuss those indeterministic processes within the individual related to emotional, social, and cognitive development. (shrink)

More and more researchers are examining grammar acquisition from theoretical perspectives that treat it as an emergent phenomenon. In this essay, I argue that a robustly developmental perspective provides a potential explanation for some of the well-known crosslinguistic features of early child language: the process of acquisition is shaped in part by the developmental constraints embodied in von Baer’s law of development. An established model of development, the Developmental Lock, captures and elucidates the probabilistic generalizations at the heart of von (...) Baer’s law. When this model is applied to the acquisition of grammar, it predicts that grammatical achievements that are more generatively entrenched will emerge earlier in development and will be more developmentally resilient than those that are less generatively entrenched. I show that the first prediction is supported by a wealth of psycholinguistic evidence involving typically developing children and that the second prediction is supported by numerous studies involving both children who receive deficient linguistic input and children who experience various language impairments. The success of this model demonstrates the analytic potential of a developmental approach to the study of language acquisition. (shrink)

Many contemporary theories of human cognition focus on the biochemical mechanisms that lie beneath the mind’s operations, while neglecting the historical and developmental aspects of the human mind. This article argues (1) that a processual form of thinking has been developing since the Modern Era. Furthermore, it maintains (2) that this particular form of thinking is intrinsically connected with the historical phenomenon of the scientific revolution. The paper studies Günter Dux’s innovative historico-genetic approach to the development of thought in historical (...) process. It also analyses the processual form of thinking under specific conceptual aspects of Alfred North Whitehead’s philosophy of organism. The present study also reveals (3) the connection between the developmental and the historical aspects of the evolution of thought. Overall, the study found (4) that there is an anthropological cognitive mechanism behind the historical forms of thought usually related to the elaborated figure of explanation. (shrink)

Comparing engineering to evolution typically involves adaptationist thinking, where well-designed artifacts are likened to well-adapted organisms, and the process of evolution is likened to the process of design. A quite different comparison is made when biologists focus on evolvability instead of adaptationism. Here, the idea is that complex integrated systems, whether evolved or engineered, share universal principles that affect the way they change over time. This shift from adaptationism to evolvability is a significant move for, as I argue, we can (...) make sense of these universal principles without making any adaptationism claims. Furthermore, evolvability highlights important aspects of engineering that are ignored in the adaptationist debates. I introduce some novel engineering examples that incorporate these key neglected aspects, and use these examples to challenge some commonly cited contrasts between engineering and evolution, and to highlight some novel resemblances that have gone unnoticed. (shrink)

Ever since Darwin a great deal of the conceptual history of biology may be read as a struggle between two philosophical positions: reductionism and holism. On the one hand, we have the reductionist claim that evolution has to be understood in terms of changes at the fundamental causal level of the gene. As Richard Dawkins famously put it, organisms are just ‘lumbering robots’ in the service of their genetic masters. On the other hand, there is a long holistic tradition that (...) focuses on the complexity of developmental systems, on the non-linearity of gene– environment interactions, and on multi-level selective processes to argue that the full story of biology is a bit more complicated than that. Reductionism can marshal on its behalf the spectacular successes of genetics and molecular biology throughout the 20th and 21st centuries. Holism has built on the development of entirely new disciplines and conceptual frameworks over the past few decades, including evo-devo and phenotypic plasticity. Yet, a number of biologists are still actively looking for a way out of the reductionism–holism counterposition, often mentioning the word ‘emergence’ as a way to deal with the conundrum. This paper briefly examines the philosophical history of the concept of emergence, distinguishes between epistemic and ontological accounts of it, and comments on conceptions of emergence that can actually be useful for practising evolutionary biologists. (shrink)

In 1961, Ernst Mayr published a highly influential article on the nature of causation in biology, in which he distinguished between proximate and ultimate causes. Mayr argued that proximate causes (e.g. physiological factors) and ultimate causes (e.g. natural selection) addressed distinct ‘how’ and ‘why’ questions and were not competing alternatives. That distinction retains explanatory value today. However, the adoption of Mayr’s heuristic led to the widespread belief that ontogenetic processes are irrelevant to evolutionary questions, a belief that has (1) hindered (...) progress within evolutionary biology, (2) forged divisions between evolutionary biology and adjacent disciplines and (3) obstructed several contemporary debates in biology. Here we expand on our earlier (Laland et al. in Science 334:1512–1516, 2011) argument that Mayr’s dichotomous formulation has now run its useful course, and that evolutionary biology would be better served by a concept of reciprocal causation, in which causation is perceived to cycle through biological systems recursively. We further suggest that a newer evolutionary synthesis is unlikely to emerge without this change in thinking about causation. (shrink)

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...) the need for a different conceptual treat- ment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable soft- ware. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem. (shrink)

Although the construction of neo-Darwinism grew out of Thomas Hunt Morgan's melding of Darwinism and Mendelism, his evidence did not soley support a model of gradual change. To the contrary, he was confronted with observations that could have led him to a more "evo-devo" understanding of the emergence of novel features. Indeed, since Morgan was an embryologist before he became a fruit-fly geneticist, one would have predicted that the combination of these two lines of research would have resulted in early (...) formulations of concepts relevant to evolutionary developmental biology. It is thus of interest to review Morgan's thought processes and arguments for at first rejecting both Darwinism and Mendelism, and then for later dismissing data that would have yielded a model of rapid morphological change in favor of a model of change based on the accumulation of minor mutations and their morphological consequences. (shrink)

Darwinists classify biological traits either by their ancestry (homology) or by their adaptive role. Only the latter can provide traditional natural kinds, but only the former is practicable. Process structuralists exploit this embarrassment to argue for non-Darwinian classifications in terms of underlying developmental mechanisms. This new taxonomy will also explain phylogenetic inertia and developmental constraint. I argue that Darwinian homologies are natural kinds despite having historical essences and being spatio-temporally restricted. Furthermore, process structuralist explanations of biological form require an unwarranted (...) assumption about the space of developmental possibility. (shrink)

The recent discovery of a phenomenon of craniofacial growth, called craniofacial contraction, throws a new light on the process of hominization. The main interest of this discovery lies in a growth principle combining the different craniofacial units, that is to say, the neurocranium, the chondrocranium and the splanchnocranium. Until recent years, these different parts were considered as neighbouring element without any morphogenic or morphodynamic connection. But now, we know that the morphogenesis of the base of the skull governs that of (...) the face. This basicranial morphogenesis is the occipital flexion. It generates morphogenic correlations with the face since embryogenesis. The ontogenic pathway of this phenomenon is the craniofacial contraction. It concerns embryonic dynamics connected with the spatial development of the embryonic neural system, the neural tube. These morphodynamics are common to each primate species, but they are differenciated by the amplitude of the embryonic contraction. We ask ourself the question: is hominization of the neurocephalic embryogenesis, that is the craniofacial contraction, plausible over a very long period, with gradual and chaotic evolutionary pathways, or, on the contrary, is the complexity of such an embryonic phenomenon, a limiting factor generating determined and predictible ontogenic thresholds? The study of extant and fossil primate skulls demonstrates that species are organized around 6 levels of embryonic contraction, which, starting from 60 millions years, evolve from the less to the most contracted skull. Among each ontogenic level, living and fossil species develop from the same embryonic system but between both levels, the embryos suddenly are reorganized. Therefore, I have defined an evolutive ontogenic unity, that is the fundamental ontogenesia. The cephalic pole has a fundamental ontogenesis, meaning that, beyond the diversities, we can see the same contraction in many living and extinct species. The ontogenic diversities are the result of the microevolution and are not predictible. In such a perspective, the ontogenic morphodynamics evolve with chaotic trajectories. But, between two embryonic levels, or two fundamental ontogeneses, evolutionary modalities are different. Eventually, from 60 millions years to XXth century, we observe the same phenomenon than during human ontogenesis; hominization of the cephalic pole is a craniofacial contraction. The evolutive pathway is stable, whatever the number of thresholds, the cranial shape changes but the ontogenic trajectory is preserved. This is a macroevolution because the embryonic system is reorganized. The logics of the phenomenon are an increasing dynamization, the human ontogenesis is the more unstable and the longer morphodynamics to stabilize the craniofacial contraction. To conclude, hominization is an iteration of an ontogenic process when embryos reach successive dynamic thresholds. The attractors are neither static, periodic, nor chaotic because the successive ontogenic trajectories are themselves in a stable evolutive trajectory, and the results with increasing contraction, complexified neocortical tissues and cephalocaudal reorganization are predictible. During hominization, irreversibility and innovations do not emerge with chaotic determinism, but with harmonic determinism in association with the correlations established between the embryonic tissues. When the system is destabilized, the embryonic systems do not forget the previous ontogenic pattern, on the contrary, they develop the pattern with new dynamical conditions. This sort of phenomenon is not described in the sciences of complexity. In the present case, we are in front of many millions years and the necessity to propose new concepts such as a new familly of attractors, namely the harmonic attractors. (shrink)

This paper examines a new challenge to neo-Darwinism, a movement known as process structuralism. The process structuralist critique of neo-Darwinism holds 1) that there are general laws in biology and that biologists should search for these laws; 2) that there are general forms of morphology and development and that biologists should attempt to uncover these forms; 3) that organisms are unified wholes that cannot be understood without adopting a holistic perspective; and 4) that no special, causal primacy should be given (...) to the genes in development and morphology. This paper places process structuralism in its historical context, examines the philosophical underpinnings of the movement, and discusses some of the evidence used to support its claims. (shrink)

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ and (...) ‘part of ’. (shrink)

Systems Biology and the Modern Synthesis are recent versions of two classical biological paradigms that are known as structuralism and functionalism, or internalism and externalism. According to functionalism (or externalism), living matter is a fundamentally passive entity that owes its organization to external forces (functions that shape organs) or to an external organizing agent (natural selection). Structuralism (or internalism), is the view that living matter is an intrinsically active entity that is capable of organizing itself from within, with purely internal (...) processes that are based on mathematical principles and physical laws. At the molecular level, the basic mechanism of the Modern Synthesis is molecular copying, the process that leads in the short run to heredity and in the long run to natural selection. The basic mechanism of Systems Biology, instead, is self-assembly, the process by which many supramolecular structures are formed by the spontaneous aggregation of their components. In addition to molecular copying and self-assembly, however, molecular biology has uncovered also a third great mechanism at the heart of life. The existence of the genetic code and of many other organic codes in Nature tells us that molecular coding is a biological reality and we need therefore a framework that accounts for it. This framework is Code biology, the study of the codes of life, a new field of research that brings to light an entirely new dimension of the living world and gives us a completely new understanding of the origin and the evolution of life. (shrink)

Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing (...) view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the "mutational landscape" model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. REVIEWERS: Alex Kondrashov, Eugene Koonin and Johann Peter Gogarten reviewed this article. (shrink)

The classic view of evolution as "shifting gene frequencies" in the Modern Synthesis literally means that evolution is the modulation of existing variation ("standing variation"), as opposed to a "new mutations" view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of (...) mutation as a cause of nonrandomness, a role that could be important but has been misconceived and associated misleadingly with neutral evolution. Specifically, biases in the introduction of variation, including mutational biases, may impose predictable biases on evolution, with no necessary dependence on neutrality. As an example of how important such effects may be, we present a new analysis partitioning the variance in mean rates of amino acid replacement during human-chimpanzee divergence to components of codon mutation and amino acid exchangeability. The results indicate that mutational effects are not merely important but account for most of the variance explained. The challenge that such results pose for comparative genomics is to address mutational effects as a necessary part of any analysis of causal factors. To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects. (shrink)

The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing (...) orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change. (shrink)

The neutral theory often is presented as a theory of "noise" or silent changes at an isolated "molecular level", relevant to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless, precisely these issues can be addressed in neutral models, such as those elaborated here in regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes. All of these are instances of (...) a more general scheme of "constructive neutral evolution" that invokes biased variation, epistatic interactions, and excess capacities to account for a complex series of steps giving rise to novel structures or operations. The directional and constructive outcomes of these models are not due to neutral allele fixations per se, but to these other factors. Neutral models of this type may help to clarify the poorly understood role of non-selective factors in evolutionary innovation and directionality. (shrink)